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Funding Update: May 27, 2011

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NSF Bioinformatics Grants Awarded April 28 — May 25, 2011

Novel Methodologies for Genome-scale Evolutionary Analysis of Multi-locus data
Start Date: July 1, 2011
Expires: June 30, 2014
This grant was awarded to three investigative teams:
$349,999, Tandy Warnow, C. Randal Linder, University of Texas, Austin
$467,429, Noah Rosenberg, University of Michigan, Ann Arbor
$425,000, Luay Nakhleh, Rice University

The funds support the development and implementation of algorithms and software to analyze gene genealogies or gene trees. The investigators will develop computational methods for determining the causes of gene tree discordance, and inferring species phylogenies from gene trees despite their discordance from genome-scale datasets.


Semiparametric conditional graphical models with applications to gene network analysis
Start Date: July 1, 2011
Expires: June 30, 2012
This grant was awarded to three investigative teams:
$25,667, Hongyu Zhao, Yale University
$54,977, Li Bing, Pennsylvania State University, University Park
$9,389, Hyonho Chun, Purdue University

Supports the development of a conditional Gaussian graphical model for constructing gene networks that incorporates information other than expression data. Although they are beginning with gene networks, the investigators believe their approach could have applications beyond genomics, such as in predicting asset returns and in studying social networks.


Statistical Methodology and Applications to Economics, Engineering and Genetics
Start Date: July 1, 2011
Expires: June 30, 2012
Awarded Amount to Date: $128,100
Principal Investigators: Tze Lai, David Siegmund
Sponsor: Stanford University

Supports the development of sequential Monte Carlo and Bayesian methods for identifying genomic regions containing a gene or genes that affect traits of interest in either humans or in experimental organisms. These methods could also be applied to engineering, finance, insurance, risk management, and surveillance.


Population Genomics of Cold Adaptation in Poplar
Start Date: March 23, 2011
Expires: Aug. 31, 2012
Awarded Amount to Date: $441,650
Principal Investigator: Matthew Olson
Sponsor: Texas Tech University

The funds will support the development of tools to identify the genetic basis for phenotypic variation in bud set — an important determinant of cold adaptation and growth rate — in Populus balsamifera, the Ontario balsam poplar. The investigators will test whether the same genes are responsible for variation and adaptive evolution of bud set in North American P. balsamifera and the European aspen P. tremula.


A Theoretical and Computational Framework for Linking Tree form and Function to Forest Diversity and Productivity
Start Date: Dec. 15, 2010
Expires: May 31, 2011
Awarded Amount to Date: $213,189
Principal Investigator: Kiona Ogle
Sponsor: Arizona State University

Supports the development of a scaling framework for understanding forest diversity and productivity. The investigators aim to develop data-model integration methodologies, including dynamic process models that link tree form and function, incorporate key plant functional traits, and are applicable to broad spatial and temporal scales; new meta-analysis methods for analyzing vast amounts of literature on species-specific traits that incorporate phylogenetic relationships and overcome limitations common to classical meta-analytic approaches; and rigorous statistical and computational methods for informing the process model with large and disparate data sources.


The Scan

Study Tracks Off-Target Gene Edits Linked to Epigenetic Features

Using machine learning, researchers characterize in BMC Genomics the potential off-target effects of 19 computed or experimentally determined epigenetic features during CRISPR-Cas9 editing.

Coronary Artery Disease Risk Loci, Candidate Genes Identified in GWAS Meta-Analysis

A GWAS in Nature Genetics of nearly 1.4 million coronary artery disease cases and controls focused in on more than 200 candidate causal genes, including the cell motility-related myosin gene MYO9B.

Multiple Sclerosis Contributors Found in Proteome-Wide Association Study

With a combination of genome-wide association and brain proteome data, researchers in the Annals of Clinical and Translational Neurology tracked down dozens of potential multiple sclerosis risk proteins.

Quality Improvement Study Compares Molecular Tumor Boards, Central Consensus Recommendations

With 50 simulated cancer cases, researchers in JAMA Network Open compared molecular tumor board recommendations with central consensus plans at a dozen centers in Japan.